5AYU | pdb_00005ayu

Crystal structure of HyHEL-10 Fv

• PDB DOI: https://doi.org/10.2210/pdb5AYU/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-09-04 Released: 2016-09-07 
• Deposition Author(s): Nakanishi, T., Tsumoto, K., Yokota, A., Kondo, H., Kumagai, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of HyHEL-10 Fv

Nakanishi, T., Tsumoto, K., Yokota, A., Kondo, H., Kumagai, I.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.72 kDa 
• Atom Count: 1,909 
• Modeled Residue Count: 220 
• Deposited Residue Count: 220 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lysozyme binding Ig kappa chain V23-J2 region	A [auth L]	107	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig VH,anti-lysozyme	B [auth H]	113	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth L], D [auth H], E [auth H], F [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.822	α = 90
b = 65.822	β = 90
c = 96.321	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
MOLREP	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-07 
Deposition Author(s): Nakanishi, T., Tsumoto, K., Yokota, A., Kondo, H., Kumagai, I.

Revision History  

• Version 1.0: 2016-09-07
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary